NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata
dc.contributor.author | Vos, Rutger A. | |
dc.contributor.author | Balhoff, James P. | |
dc.contributor.author | Caravas, Jason A. | |
dc.contributor.author | Holder, Mark T. | |
dc.contributor.author | Lapp, Hilmar | |
dc.contributor.author | Maddison, Wayne P. | |
dc.contributor.author | Midford, Peter E. | |
dc.contributor.author | Priyam, Anurag | |
dc.contributor.author | Sukumaran, Jeet | |
dc.contributor.author | Xia, Xuhua | |
dc.contributor.author | Stoltzfus, Arlin | |
dc.date.accessioned | 2014-04-10T20:16:10Z | |
dc.date.available | 2014-04-10T20:16:10Z | |
dc.date.issued | 2012-02-22 | |
dc.identifier.citation | Vos, Rutger A, James P Balhoff, Jason A Caravas, Mark T Holder, Hilmar Lapp, Wayne P Maddison, Peter E Midford, et al. 2012. “NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata.” Systematic Biology 61 (4): 675–89. http://dx.doi.org/10.1093/sysbio/sys025. | |
dc.identifier.uri | http://hdl.handle.net/1808/13438 | |
dc.description.abstract | In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input–output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML. | |
dc.description.sponsorship | R.A.V. received support from the CIPRES project (NSF #EF-03314953 to W.P.M.), the FP7 Marie Curie Programme (Call FP7-PEOPLE-IEF-2008—Proposal No. 237046) and, for the NeXML implementation in TreeBASE, the pPOD project (NSF IIS 0629846); P.E.M. and J.S. received support from CIPRES (NSF #EF-0331495, #EF-0715370); M.T.H. was supported by NSF (DEB-ATOL-0732920); X.X. received support from NSERC (Canada) Discovery and RTI grants; W.P.M. received support from an NSERC (Canada) Discovery grant; J.C. received support from a Google Summer of Code 2007 grant; A.P. received support from a Google Summer of Code 2010 grant. | |
dc.publisher | Oxford University Press | |
dc.rights | This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. | |
dc.rights.uri | http://creativecommons.org/licenses/by-nc/3.0 | |
dc.subject | Data Standards | |
dc.subject | Evolutionary Informatics | |
dc.subject | Interoperability | |
dc.subject | Phyloinformatics | |
dc.subject | Semantic Web | |
dc.subject | Syntax Format | |
dc.title | NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata | |
dc.type | Article | |
kusw.kuauthor | Holder, Mark T. | |
kusw.kuauthor | Sukumaran, Jeet | |
kusw.kudepartment | Department of Ecology and Evolutionary Biology | |
kusw.oastatus | fullparticipation | |
dc.identifier.doi | 10.1093/sysbio/sys025 | |
kusw.oaversion | Scholarly/refereed, publisher version | |
kusw.oapolicy | This item meets KU Open Access policy criteria. | |
dc.rights.accessrights | openAccess |
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